top of page


Abhilash, L. and Shafer, O.T., (2022) A two-process model of Drosophila sleep reveals an inter-dependence between circadian clock speed and the rate of sleep pressure decay. bioRxiv 2022.08.12.503775; DOI: 10.1101/2022.08.12.503775

Chowdhury, B., Abhilash L., Ortega, A. Liu, S., and Shafer, O.T., (2022) Homeostatic Control of Deep sleep in Drosophila: Implications for Discovering Correlates of Sleep Pressure. bioRxiv 2022.09.30.510368; DOI: 10.1101/2022.09.30.510368

Abhilash, L., and Shafer, O.T., (2023) Parametric effects of light acting via multiple photoreceptor types contribute significantly to circadian entrainment in Drosophila melanogaster. Proc. R. Soc. B. 290: 20230149 [PMID: 37700655]

Emery, P., Klarsfeld, A., Stanewsky, R., and Shafer O.T. (2023) Sensitive Timing: A Reappraisal of Chronobiology's Foundational Texts. J. Biol. Rhythm. 38: 245-258 [PMID: 37226809]

Shafer, O.T., Gutierrez G.J., Li, K., Mildenhall, A., Spira, D., Marty, J., Lazar, A.A., and Fernandez M.P., (2022) Connectomic Analysis of the Drosophila Lateral Neuron Clock Cells Reveals the Synaptic Basis of Functional Pacemaker Classes. eLife 11:e79139  [PMID: 35766361]

Persons, J.L., Abhilash, L., Lopatkin, A.J., Roelofs, A., Bell, E.V., Fernandez, M.P., and Shafer O.T. (2022) PHASE: An Open-Source Program for the Analysis of Drosophila Phase, Activity and Sleep Under Entrainment. J. Biol. Rhythm. 37: 455-467 [PMID: 35727044]

B Kostadinov, HL Pettibone, EV Bell, X Zhou, A Pranevicius, OT Shafer and Fernandez, MP (2021). Open-source computational framework for studying Drosophila behavioral phase. STAR protocols 2 (1), 100285

OT Shafer, AC Keene (2021). The Regulation of Drosophila Sleep. Current Biology 31 (1), R38-R49

Florencia Fernandez-Chiappe, Christiane Hermann-Luibl, Alina Peteranderl, Nils Reinhard, Pingkalai R Senthilan, Marie Hieke, Mareike Selcho, Taishi Yoshii, Orie T Shafer, Nara I Muraro, Charlotte Helfrich-Förster (2020) . Dopamine Signaling in Wake-Promoting Clock Neurons Is Not Required for the Normal Regulation of Sleep in Drosophila. Journal of Neuroscience 40 (50), 9617-9633

B Chowdhury, OT Shafer (2020). Why the young sleep longer. Elife 9, e56833

Anthony Fiorino, Dakotah Thompson, Swathi Yadlapalli, Chang Jiang, Orie T Shafer, Pramod Reddy, Edgar Meyhofer. Parallelized, real-time, metabolic-rate measurements from individual Drosophila. Scientific reports 8 (1), 1-10

IU Hsu, JW Linsley, JE Varineau, OT Shafer, JY Kuwada (2018). Dstac is required for normal circadian activity rhythms in Drosophila. Chronobiology international 35 (7), 1016-1026

Fernández MP, Pettibone HL, Bogart JT, Roell CJ, Davey CE, Pranevicius A, Huynh KV, Lennox SM, Kostadinov BS and Shafer OT. (2020) Sites of Circadian Clock Neuron Plasticity Mediate Sensory Integration and Entrainment in Drosophila. Current Biology 30, 2225–2237.

Yadlapalli, S., Jiang, C., Bahle, A., Reddy, P., Meyhofer, E., Shafer, O.T. (2018). Circadian clock neurons constantly monitor environmental temperature to set sleep timing. Nature. doi: 10.1038/nature25740. PubMed

Yadlapalli, S., Shafer, O.T. (2017). Thermoregulation: How a brain keeps its cool. eLife. 2017;6:e28109. doi: 10.7554/eLife.28109. PubMed

Abruzzi, K.C., Zadina, A., Luo, W., Wiyanto, E., Rahman, R., Guo, F., Shafer, O., Rosbash, M. (2017). RNA-seq analysis of Drosophila clock and non-clock neurons reveals neuron-specific cycling and novel candidate neuropeptides. PLoS Genetics, 13(2), [e1006613]. doi: 10.1371/journal.pgen.1006613. PubMed

Yao, Z., Bennett, A. J., Clem, J. L., & Shafer, O. T. (2016). The Drosophila Clock Neuron Network Features Diverse Coupling Modes and Requires Network-wide Coherence for Robust Circadian Rhythms. Cell Reports, 17(11), 2873-2881. doi: 10.1016/j.celrep.2016.11.053. PubMed

Schlichting, M., Menegazzi, P., Lelito, K.R., Yao, Z., Buhl, E., Benetta, E.D., Bahle, A., Denike, J., Hodge, J.J., Helfrich-Förster, C., Shafer, O.T. (2016). A neural network underlying circadian entrainment and photoperiodic adjustment of sleep and activity in Drosophila. Journal of Neuroscience, 36(35), 9084-9096. doi: 10.1523/JNEUROSCI.0992-16.2016. PubMed

Oh, Y., Yoon, S. E., Zhang, Q., Chae, H. S., Daubnerová, I., Shafer, O. T., Choe, J., Kim, Y. J. (2014). A Homeostatic Sleep-Stabilizing Pathway in Drosophila Composed of the Sex Peptide Receptor and Its Ligand, the Myoinhibitory Peptide. PLoS Biology, 12(10). doi: 10.1371/journal.pbio.1001974. PubMed

Collins, B., Kaplan, H. S., Cavey, M., Lelito, K. R., Bahle, A. H., Zhu, Z., Macara, A.M., Roman, G., Shafer, O.T., Blau, J. (2014). Differentially Timed Extracellular Signals Synchronize Pacemaker Neuron Clocks. PLoS Biology, 12(9). doi: 10.1371/journal.pbio.1001959. PubMed

Shafer, O. T., & Yao, Z. (2014). Pigment-dispersing factor signaling and circadian rhythms in insect locomotor activity. Current Opinion in Insect Science, 1, 73-80. doi: 10.1016/j.cois.2014.05.002. PubMed

Yao, Z. and Shafer, O.T. (2014). The Drosophila Circadian Clock Is a Variably Coupled Network of Multiple Peptidergic Units. Science. 343(6178): 1516-1520. doi: 10.1126. PubMed

Talsma, A.D., Christov, C.P., Terriente-Felix, A., Linneweber, G.A., Perea, D., Wayland, M., Shafer, O.T., and Miguel-Aliaga, I. (2012). Remote control of renal physiology by the intestinal neuropeptide pigment-dispersing factor in Drosophila. PNAS. July 9, 2012, doi: 10.1073/pnas.1200247109. PubMed

Yao, Z., Macara, A.M., Lelito, K.R., Minosyan, T., and Shafer, O.T. (2012). Analysis of Functional Neuronal Connectivity in the Drosophila Brain. J Neurophysiol. [Epub ahead of print]. PubMed

Lelito, K.R., and Shafer, O.T. (2012). Reciprocal Cholinergic and GABAergic Modulation of the Small Ventrolateral Pacemaker Neurons of Drosophila’s Circadian Clock Neuron Network. J Neurophysiol. Jan 25. Epub ahead of print. PubMed

Beckwith, E.J., Lelito, K.R., Hsu, Y.W., Medina, B.M., Shafer, O.T., Ceriani, M.F., and de la Iglesia, H.O. (2011). Functional conservation of clock output signaling between flies and intertidal crabs. J Biol Rhythms. 26(6):518-29. PubMed

Shafer, O.T., and Taghert, P.H. (2009). RNA-interference knockdown of Drosophila pigment dispersing factor in neuronal subsets: the anatomical basis of a neuropeptide’s circadian functions. PLoS One. 4(12):e8298. PubMed

Shafer, O.T., Kim, D.J., Dunbar-Yaffe, R., Nikolaev, V.O., Lohse, M.J., and Taghert, P.H. (2008). Widespread receptivity to neuropeptide PDF throughout the neuronal circadian clock network of Drosophila revealed by real-time cyclic AMP imaging. Neuron. 58:223-237. PubMed

Park, D., Shafer, O.T., Shepherd, S.P., Suh, H., Trigg, J.S., and Taghert, P.H. (2008). The Drosophila basic helix-loop-helix protein DIMMED directly activates PHM, a gene encoding a neuropeptide-amidating enzyme. Mol Cell Biol. 28:410-421. PubMed

Helfrich-Förster, C., Shafer, O.T., Wulbeck, C., Grieshaber, E., Rieger, D., and Taghert, P.H. (2007). Development and morphology of the clock-gene-expressing lateral neurons of Drosophila melanogaster. J. Comp. Neurol. 500:47-70. PubMed

Shafer, O.T., Helfrich-Förster, C., Renn, S.C.P., and Taghert, P.H. (2006). Re-evaluation of Drosophila melanogaster’s neuronal circadian pacemakers reveals new neuronal classes. Journal of Comparative Neurology. 498:180-93. PubMed

Rieger, D., Shafer, O.T., Tomioka, K., and Helfrich-Förster, C. (2006). Functional analysis of circadian pacemaker neurons in Drosophila melanogaster. Journal of Neuroscience. 26:2531-43. PubMed

Taghert, P.H., and Shafer, O.T. (2006). Mechanisms of clock output in the Drosophila circadian pacemaker system. J. Biol. Rhythms. 21:445-57. PubMed

Mertens*, I., Vandingenen*, A., Johnson* E.C., Shafer*, O.T., Li W., Trigg, J.S., De Loof, A., Schoofs, L., and Taghert, P.H. (2005). PDF receptor signaling in Drosophila contributes to both circadian and geotactic behaviors. Neuron. 48: 213-119. PubMed

Johnson, E.C., Shafer, O.T., Trigg, J.S., Park, J., Schooley, D.A., Dow, J.A., and Taghert P.H. (2005). A novel diuretic hormone receptor in Drosophila: evidence for conservation of CGRP signaling. Journal of Experimental Biology. 208:1239-46. PubMed

Wülbeck, C., Szabo, G., Shafer, O.T., Helfrich-Förster, C., and Stanewsky, R. (2005). The novel Drosophila tim(blind) mutation affects behavioral rhythms but not periodic eclosion. Genetics. 169:751-66. PubMed

Shafer*, O.T., Levine*, J.D., Truman, J.W., and Hall, J.C. (2004). Flies By Night: Effects of Changing Day Length on Drosophila’s Circadian Clock . Current Biology. 14: 424-432. PubMed

Shafer, O.T., Rosbash, M.R., and Truman, J.W. (2002). Sequential Nuclear Accumulation of the Clock Proteins Period and Timeless in the Pacemaker Neurons of Drosophila melanogaster. Journal of Neuroscience. 22: 5946-5954. PubMed

Shafer, O.T. (2001). Blind clocks reveal elusive light input pathway in Drosophila. Trends in Neurosciences. 24:626-628. PubMed

Publications: Overview
bottom of page